Contacts of the helix formed by residues 432 - 448 (chain B) in PDB entry 1JZ3
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TRP 432 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B PRO* 3.8 36.6 - - + +
111B PRO* 4.1 22.4 - - + +
112B PRO* 4.5 4.7 - - + -
193B ASP* 3.7 27.1 - - + -
196B TYR* 3.8 13.0 - + + -
197B LEU* 3.8 41.5 - - + -
426B LEU* 3.4 46.8 - - + +
429B ASP* 3.0 24.5 + - + -
430B PRO 3.0 0.8 - - - -
431B ARG* 1.3 82.3 - - + +
433B LEU* 1.3 64.3 + - - +
434B PRO 3.3 2.7 - - - -
435B ALA* 3.6 9.7 + - + +
436B MET* 3.1 28.8 + - - +
467B ASN* 3.6 3.4 - - - +
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Residues in contact with LEU 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B PRO* 3.0 14.0 + - + +
432B TRP* 1.3 78.6 - - - +
434B PRO* 1.3 63.8 - - + +
436B MET 3.2 0.5 + - - -
437B SER* 2.7 35.6 + - - -
467B ASN* 3.3 41.1 - - + +
470B ALA* 4.5 8.1 - - + -
471B LEU* 4.3 23.8 - - + -
433C LEU* 5.7 6.3 - - + -
437C SER* 3.9 26.9 - - - +
441C THR* 4.8 5.8 - - + -
471C LEU* 4.5 10.1 - - + -
474C TRP* 4.3 22.2 - - + +
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Residues in contact with PRO 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B PRO 5.1 5.6 - - - +
20B GLY* 5.8 4.9 - - - -
22B THR* 5.4 0.4 - - - -
430B PRO 3.3 12.8 - - - +
431B ARG* 3.7 9.9 - - - +
432B TRP 3.5 2.9 - - - -
433B LEU* 1.3 95.7 - - + +
435B ALA* 1.3 62.0 + - - +
437B SER* 2.9 23.1 + - - +
438B GLU* 3.2 13.9 + - - +
433C LEU* 6.4 0.2 - - + -
434C PRO* 3.6 39.4 - - + +
437C SER* 4.4 7.0 - - - +
438C GLU* 4.9 11.4 - - + +
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Residues in contact with ALA 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B PRO* 3.8 14.3 + - + +
22B THR* 3.8 29.4 - - + +
163B GLN* 6.1 0.2 - - - +
193B ASP* 5.6 1.1 - - - +
197B LEU* 4.1 19.3 - - + -
431B ARG 5.4 0.2 + - - -
432B TRP* 3.6 17.6 + - + +
433B LEU 3.5 0.4 - - - -
434B PRO* 1.3 77.5 - - - +
436B MET* 1.3 63.8 + - - +
438B GLU* 3.4 10.8 + - - +
439B ARG* 3.5 20.1 + - - +
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Residues in contact with MET 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B LEU* 4.4 17.3 - - + -
415B ILE* 3.8 34.6 - - + +
426B LEU 4.5 2.2 - - - +
427B THR* 3.6 35.7 - - + -
432B TRP* 3.1 19.2 + - + +
433B LEU* 3.7 3.6 - - - +
435B ALA* 1.3 75.6 - - - +
437B SER* 1.3 70.6 + - - +
439B ARG* 3.0 13.4 + - - +
440B VAL 3.3 7.4 + - - -
467B ASN* 3.5 41.3 - - + -
468B HIS* 4.1 21.8 - - + +
471B LEU* 3.8 14.4 - - + +
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Residues in contact with SER 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B LEU* 2.7 22.2 + - - -
434B PRO* 2.9 17.5 + - - +
436B MET* 1.3 76.3 - - - +
438B GLU* 1.3 54.7 + - - +
440B VAL* 3.1 1.7 + - - +
441B THR* 2.7 41.0 + - - +
471B LEU* 3.4 30.3 - - - +
430C PRO 5.5 0.7 + - - -
433C LEU* 3.9 23.6 - - - +
434C PRO* 4.8 5.5 - - - +
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Residues in contact with GLU 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B THR* 2.5 33.0 + - + -
23B GLN* 4.4 10.5 + - - +
26B ARG* 3.0 23.5 + - - +
164B ASP* 4.7 2.1 - - + +
167B LEU* 4.4 0.7 - - - +
434B PRO 3.2 13.4 + - - +
435B ALA 3.9 6.7 - - - +
436B MET 3.2 0.4 - - - -
437B SER* 1.3 80.5 + - - +
439B ARG* 1.4 64.4 + - + +
441B THR* 3.6 8.1 - - - +
442B ARG* 3.1 42.7 + - + +
431C ARG* 6.0 1.9 + - - -
434C PRO* 5.0 11.9 - - + +
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Residues in contact with ARG 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B THR* 6.0 3.0 - - - +
163B GLN* 4.6 4.2 - - - +
164B ASP* 3.3 42.6 - - + +
167B LEU* 3.9 6.1 - - - +
194B GLY* 3.5 25.9 - - - -
197B LEU* 3.5 28.6 - - - +
198B GLU* 2.9 35.9 + - - +
393B PRO* 5.0 0.2 - - - +
413B ALA* 3.7 11.5 - - - +
414B ASN* 2.9 39.8 + - - +
415B ILE* 3.7 18.2 - - + -
435B ALA* 3.5 14.9 + - - +
436B MET 3.0 8.2 + - - +
438B GLU* 1.4 79.7 - - + +
440B VAL* 1.4 59.2 + - - +
443B MET* 3.5 17.0 - - - +
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Residues in contact with VAL 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B ALA* 3.9 20.4 - - + -
415B ILE* 4.2 6.7 - - + -
436B MET 3.3 3.7 + - - +
437B SER 3.1 6.3 + - - +
439B ARG* 1.4 77.5 - - - +
441B THR* 1.3 71.3 + - + +
442B ARG 3.3 0.2 - - - -
443B MET* 3.1 16.7 + - + +
444B VAL* 3.2 13.1 + - + +
458B LEU* 4.2 15.9 - - + +
471B LEU* 3.9 31.2 - - + -
474B TRP* 4.3 5.6 - - + -
475B ILE* 3.6 36.8 - - + -
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Residues in contact with THR 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B SER* 2.7 35.3 + - - +
438B GLU* 3.6 9.5 - - - +
440B VAL* 1.3 75.4 - - + +
442B ARG* 1.3 63.5 + - - +
444B VAL* 3.3 2.4 + - - +
445B GLN* 3.0 33.2 + - - +
471B LEU* 5.1 1.1 - - + -
474B TRP* 3.5 50.1 - - + +
430C PRO* 4.0 22.2 - - + +
433C LEU* 4.8 3.6 - - + -
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Residues in contact with ARG 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ARG* 3.4 51.5 - - - +
27B LEU 4.9 4.2 + - - -
29B ALA* 4.0 28.9 - - + +
163B GLN 4.5 0.2 + - - -
164B ASP* 4.4 10.9 + - - +
167B LEU* 3.7 39.3 + - + +
168B PRO 2.8 26.2 + - - -
169B SER* 4.1 0.2 - - - +
170B GLU 5.3 0.2 - - - +
438B GLU* 3.1 38.1 + - - +
441B THR* 1.3 85.3 + - - +
443B MET* 1.3 64.4 + - - +
445B GLN* 3.8 12.1 - - - +
446B ARG* 3.2 21.7 + - - +
431C ARG* 6.1 1.5 - - - +
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Residues in contact with MET 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B LEU* 3.6 13.3 - - + +
393B PRO* 4.0 14.4 - - + -
411B ASP* 3.7 27.1 - - - +
412B GLU 3.5 35.4 - - - +
413B ALA* 3.5 20.2 - - + +
439B ARG 3.5 11.4 - - - +
440B VAL* 3.1 17.8 + - + +
442B ARG* 1.3 75.8 - - - +
444B VAL* 1.3 72.1 + - + +
446B ARG* 3.1 2.1 + - - +
447B ASP* 2.9 25.9 + - - +
456B TRP* 3.8 23.1 - - + -
457B SER 3.9 8.5 - - - +
475B ILE* 5.2 1.3 - - + -
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Residues in contact with VAL 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440B VAL 3.2 10.8 + - - +
441B THR 3.7 7.2 - - - +
443B MET* 1.3 84.7 - - + +
445B GLN* 1.3 64.3 + - + +
448B ARG* 3.1 43.2 + - + +
456B TRP* 3.8 43.7 - - + +
474B TRP* 3.8 27.4 - - + -
475B ILE* 4.3 15.3 - - + -
478B VAL* 4.3 12.6 - - + -
479B ASP* 4.9 5.2 - - + -
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Residues in contact with GLN 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ALA* 5.7 3.2 - - - +
29B ALA* 3.6 43.4 + - + +
30B HIS* 3.4 17.3 - - - -
31B PRO* 3.4 11.8 - - - +
224B ASP* 4.9 11.0 + - - +
441B THR 3.0 21.8 + - - +
442B ARG* 4.0 8.4 - - - +
443B MET 3.2 0.2 - - - -
444B VAL* 1.3 77.8 - - + +
446B ARG* 1.3 60.3 + - - +
448B ARG* 4.4 12.6 - - - +
474B TRP* 5.0 3.4 - - + -
430C PRO* 3.6 32.1 - - + +
431C ARG* 5.9 5.2 - - - +
8420C DMS 4.4 19.8 + - - +
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Residues in contact with ARG 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ALA* 5.6 1.8 - - + -
30B HIS 3.6 19.9 - - - +
31B PRO* 3.6 5.4 - - - +
32B PRO* 3.5 28.6 - - + +
144B ASP* 5.5 1.0 + - - -
166B ARG 4.2 5.1 + - - -
167B LEU* 3.7 13.3 - - + +
168B PRO* 3.8 38.2 - - + +
210B ARG* 4.4 2.6 - - - +
393B PRO* 3.4 9.5 - - - +
394B ASN 2.9 28.8 + - - -
396B PRO* 4.2 23.5 - - - +
399B TYR* 3.2 17.2 + - - -
442B ARG 3.2 17.1 + - - +
443B MET 3.1 2.8 + - - +
444B VAL 3.0 0.6 - - - -
445B GLN* 1.3 80.3 - - - +
447B ASP* 1.3 90.6 + - - +
448B ARG* 3.6 0.4 - - - -
449B ASN 5.0 0.7 + - - -
450B HIS* 4.8 1.2 - - - -
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Residues in contact with ASP 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B PRO* 5.7 0.9 - - - +
396B PRO* 6.0 0.2 - - - +
399B TYR* 3.3 16.3 + - - -
411B ASP* 2.3 34.3 - - - +
443B MET* 2.9 17.1 + - - +
446B ARG* 1.3 124.5 + - - +
448B ARG* 1.3 59.5 - - - +
449B ASN 3.1 3.6 - - - -
450B HIS* 3.0 38.0 + - + +
453B VAL* 4.2 6.5 - - + +
456B TRP* 4.0 8.4 - - + -
482B ARG* 4.2 2.3 + - - -
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Residues in contact with ARG 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B PRO* 5.3 0.9 - - + -
226B HIS* 3.3 60.0 + - + +
227B VAL 4.9 1.7 - - - +
444B VAL* 3.1 29.3 + - + +
445B GLN* 4.4 14.6 - - - +
446B ARG 3.6 0.6 - - - -
447B ASP* 1.3 77.1 - - - +
449B ASN* 1.4 69.7 + - - +
450B HIS 3.3 0.7 - - - -
456B TRP* 3.8 10.7 - - + -
478B VAL* 3.6 26.1 + - - +
479B ASP* 4.8 13.4 + - - +
482B ARG* 2.8 37.5 + - - +
8401B DMS 3.8 4.7 - - - +
8420C DMS 4.1 18.0 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il